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Microb Genom. 2019 Sep;5(9). doi: 10.1099/mgen.0.000293. Epub 2019 Sep 11.

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.

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Quadram Institute Bioscience and University of East Anglia, Norwich, NR4 7UA, UK.
Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK.
NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, B15 2GW, UK.
Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
McGill University, Montréal, QC H3G 2M1, Canada.
School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK.
School of Veterinary Medicine, University of Surrey, Daphne Jackson Rd, Guildford GU2 7AL, UK.


Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson's index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.


antimicrobial resistance; critical illness; gut microbiota; intensive care unit; meropenem; microbiome; pathogens; shotgun metagenomics

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